Active tree planting for rehabilitation purposes is practiced in many areas of the world. In Giant Mts. National Park and Biosphere Reserve, Czech Republic, krummholz (Pinus mugo Turra.) shrubs were planted a century ago, over previously cleared areas in the alpine tundra zones. These shrubs were planted in response to damaging flooding events. Recently, this practice has been subject to scrutiny, since the new plantations have expanded into the last post-glacial remnants of alpine tundra, threatening continued existence of the original alpine plant communities. Thus, the purpose of this study was to analyze plant communities and soils above and within the zone of planted P. mugo encroachment, and to determine the effects of krummholz shrubs on the underlying soil nutrients (exchangeable Ca, K, Mg, CEC, available P, and pH). Microclimate in both habitats was also monitored as an additional possible factor driving the ecosystem change. Alpine tundra was richer in vascular species while bryophytes and lichens were more prominent in the krummholz zone, suggesting that spreading of P. mugo decreased alpine flower diversity and abundance. Soils in both habitats were of podzolic order. Under the krummholz shrubs, the surface organic layers were significantly thicker, and the A and B mineral horizons were more developed. These soils were also slightly more acidic, and their Ah horizon was greater in nutrient content and cation exchange capacity. In comparison with the open tundra, the microclimate in the krummholz zone was cooler, slowing the decomposition processes, contributing to organic matter built-up, and indirectly increasing its acidity. The results show the potential long term effects of P. mugo plantations on the endemic alpine vegetation distribution, and on the soil. These processes were initiated over a century ago. In lieu of the new findings, a review of the old management practices in the present national park is warranted to ensure the conservation of endangered alpine tundra communities.